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PDBsum entry 1vf9
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DNA binding protein
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PDB id
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1vf9
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References listed in PDB file
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Key reference
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Title
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Comparison between trf2 and trf1 of their telomeric DNA-Bound structures and DNA-Binding activities.
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Authors
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S.Hanaoka,
A.Nagadoi,
Y.Nishimura.
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Ref.
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Protein Sci, 2005,
14,
119-130.
[DOI no: ]
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PubMed id
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Abstract
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Mammalian telomeres consist of long tandem arrays of double-stranded telomeric
TTAGGG repeats packaged by the telomeric DNA-binding proteins TRF1 and TRF2.
Both contain a similar C-terminal Myb domain that mediates sequence-specific
binding to telomeric DNA. In a DNA complex of TRF1, only the single Myb-like
domain consisting of three helices can bind specifically to double-stranded
telomeric DNA. TRF2 also binds to double-stranded telomeric DNA. Although the
DNA binding mode of TRF2 is likely identical to that of TRF1, TRF2 plays an
important role in the t-loop formation that protects the ends of telomeres.
Here, to clarify the details of the double-stranded telomeric DNA-binding modes
of TRF1 and TRF2, we determined the solution structure of the DNA-binding domain
of human TRF2 bound to telomeric DNA; it consists of three helices, and like
TRF1, the third helix recognizes TAGGG sequence in the major groove of DNA with
the N-terminal arm locating in the minor groove. However, small but significant
differences are observed; in contrast to the minor groove recognition of TRF1,
in which an arginine residue recognizes the TT sequence, a lysine residue of
TRF2 interacts with the TT part. We examined the telomeric DNA-binding
activities of both DNA-binding domains of TRF1 and TRF2 and found that TRF1
binds more strongly than TRF2. Based on the structural differences of both
domains, we created several mutants of the DNA-binding domain of TRF2 with
stronger binding activities compared to the wild-type TRF2.
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Figure 4.
Figure 4. Comparison of DNA recognition modes between hTRF1
and hTRF2. (A) DNA recognition of the DNA-binding domain of
hTRF2. The red circle indicates hydrophobic contact containing
methyl groups of Ala484, Val485, and T3. Black broken lines
indicate hydrophilic contacts between Asp489 and C7', C8'. (B)
The interaction modes of Ser404/Ser417, Ala471/Ala484, and the
phosphate group of T3. Black broken lines indicate hydrophilic
contacts. (C) The interaction modes in the minor groove of DNA.
Sidechains of Arg380 of hTRF1 and Lys447 of hTRF2, and DNA are
shown. In hTRF1, the average distances over 20 structures
between NH1 of Arg380 and O2 of T9, NH2 of Arg380 and O2 of T9,
NH1 of Arg380 and N3 of A6', and NH2 of Arg380 and N3 of A6' are
shown. In hTRF2, the average distances over 20 structures
between NZ of Lys447 and O2 of T9, and NZ of Lys447 and N3 of
A6' are shown. (D) The number of hydrogen bonds in the
determined structures of the hTRF1 complex and the hTRF2
complex, respectively. The criteria of the hydrogen bonds were
set as N-H o o D (O or N): N o o D distance < 3.5 Å; N-H-D angle
> 90°.
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Figure 5.
Figure 5. NMR titration experiments of the wild-type,
K447R, A471S, A484S, R496K, DM (A471S/A484S), and QM
(K447R/A471S/A484S/R496K) to the telomeric double-stranded DNA
with the sequence GT-TAGGGTTAGGG.
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The above figures are
reprinted
by permission from the Protein Society:
Protein Sci
(2005,
14,
119-130)
copyright 2005.
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